Subsections


Compare Immune Repertoires

Using the Compare Immune Repertoires we can compare properties such as diversity and similarity of the immune repertoires characterized by Immune Repertoire Analysis.

To run Compare Immune Repertoires go to the Toolbox and select:

        Tools | QIAseq Panel Expert Tools (Image qiaseq_expert_folder_closed_16_n_p) | QIAseq Immune Repertoire Expert Tools (Image immune_rept_folderclosed_16_n_p) | Compare Immune Repertoires (Image immune_rept_compare_16_n_p)

This opens a dialog where Immune Repertoires (Image immune_rept_table_16_n_p) generated by the Immune Repertoire Analysis tool to be compared can be selected.

Output from Compare Immune Repertoires tool

Three outputs can be generated by the Compare Immune Repertoires tool

  1. Compare Immune Repertoires Report A report containing comparisons of repertoire summary statistics, diversity, etc.
  2. Heat map A heat map with similar repertoires clustered.
  3. Similarity table A table showing the similarity of the immune repertoires for each pair of samples.

Compare Immune Repertoires Report

The Compare Immune Repertoires report contains the following sections:

The remaining information in the report is only given for those chain types for which clonotypes have been identified for at least two of the input samples.

Heat map

For each pair of samples the weighted Jaccard similarity between the two is computed. Let $ X_i$, $ Y_i$ denote the relative frequencies of the $ i$'th clonotype in the first and second sample respectively. The weighted Jaccard similarity is defined as,

$\displaystyle J(X,Y) = \frac{\sum_{i=1}^n \operatorname{min}(X_i, Y_i)}{\sum_{i=1}^n \operatorname{max}(X_i, Y_i)}$ (8.1)

The weighted Jaccard distance is defined as,

$\displaystyle D(X,Y) = 1-J(X,Y)$ (8.2)

Based on the Jaccard distance a heat map is created with the samples clustered hierarchically.

Similarity table

A table showing the Jaccard similarity (eq. 8.1) between each pair of samples.